OpenMS
2.4.0
|
An implementation of the OpenSWATH Spectrum Access interface completely in memory. More...
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h>
Public Types | |
typedef OpenMS::PeakMap | MSExperimentType |
typedef OpenMS::MSSpectrum | MSSpectrumType |
typedef OpenMS::MSChromatogram | MSChromatogramType |
Public Member Functions | |
SpectrumAccessOpenMSInMemory (OpenSwath::ISpectrumAccess &origin) | |
Constructor. More... | |
~SpectrumAccessOpenMSInMemory () override | |
Destructor. More... | |
SpectrumAccessOpenMSInMemory (const SpectrumAccessOpenMSInMemory &rhs) | |
Copy constructor. More... | |
boost::shared_ptr< OpenSwath::ISpectrumAccess > | lightClone () const override |
Light clone operator (actual data will not get copied) More... | |
OpenSwath::SpectrumPtr | getSpectrumById (int id) override |
Return a pointer to a spectrum at the given id. More... | |
OpenSwath::SpectrumMeta | getSpectrumMetaById (int id) const override |
Returns the meta information for a spectrum. More... | |
std::vector< std::size_t > | getSpectraByRT (double RT, double deltaRT) const override |
Return a vector of ids of spectra that are within RT +/- deltaRT. More... | |
size_t | getNrSpectra () const override |
Returns the number of spectra available. More... | |
OpenSwath::ChromatogramPtr | getChromatogramById (int id) override |
Return a pointer to a chromatogram at the given id. More... | |
size_t | getNrChromatograms () const override |
Returns the number of chromatograms available. More... | |
std::string | getChromatogramNativeID (int id) const override |
Returns the native id of the chromatogram at the given id. More... | |
Public Member Functions inherited from ISpectrumAccess | |
virtual | ~ISpectrumAccess () |
Destructor. More... | |
Private Attributes | |
std::vector< OpenSwath::SpectrumPtr > | spectra_ |
std::vector< OpenSwath::SpectrumMeta > | spectra_meta_ |
std::vector< OpenSwath::ChromatogramPtr > | chromatograms_ |
std::vector< std::string > | chromatogram_ids_ |
An implementation of the OpenSWATH Spectrum Access interface completely in memory.
This implementation of the spectrum access interface ensures that all data is held completely in memory and is quickly accessible. This class can be generated by passing any object implementing the Spectrum Access interface and guarantees to provide the same access to the raw data as the original object with the added benefits (and downside) of keeping all data in system memory.
A possible example
After executing this code, two variables exist: data_access which provides access to the original data but does so in one of multiple ways which is not transparent to the user. However, in_memory_data_access will provide access to the same data but with the guarantee that the data is available in memory and not read from the disk.
typedef OpenMS::PeakMap MSExperimentType |
typedef OpenMS::MSSpectrum MSSpectrumType |
|
explicit |
Constructor.
|
override |
Destructor.
SpectrumAccessOpenMSInMemory | ( | const SpectrumAccessOpenMSInMemory & | rhs | ) |
Copy constructor.
|
overridevirtual |
Return a pointer to a chromatogram at the given id.
Implements ISpectrumAccess.
|
overridevirtual |
Returns the native id of the chromatogram at the given id.
Implements ISpectrumAccess.
|
overridevirtual |
Returns the number of chromatograms available.
Implements ISpectrumAccess.
|
overridevirtual |
Returns the number of spectra available.
Implements ISpectrumAccess.
Return a vector of ids of spectra that are within RT +/- deltaRT.
Implements ISpectrumAccess.
|
overridevirtual |
Return a pointer to a spectrum at the given id.
Implements ISpectrumAccess.
|
overridevirtual |
Returns the meta information for a spectrum.
Implements ISpectrumAccess.
|
overridevirtual |
Light clone operator (actual data will not get copied)
Implements ISpectrumAccess.
|
private |
|
private |
|
private |
|
private |